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https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#1
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449068/development-of-a-novel-human-recellularized-endometrium-that-responds-to-a-28-day-hormone-treatment
#2
Susan A Olalekan, Joanna E Burdette, Spiro Getsios, Teresa K Woodruff, J Julie Kim
Three dimensional (3D) in vitro models have been established to study the physiology and pathophysiology of the endometrium. With emerging evidence that the native extracellular matrix (ECM) provides appropriate cues and growth factors essential for tissue homeostasis, we describe, a novel 3D endometrium in vitro model developed from decellularized human endometrial tissue repopulated with primary endometrial cells. Analysis of the decellularized endometrium using mass spectrometry analysis revealed an enrichment of cell adhesion molecules, cytoskeletal proteins and ECM proteins such as Collagen IV and Laminin...
April 25, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28449041/periodontal-disease-tooth-loss-and-cancer-risk
#3
Dominique S Michaud, Zhuxuan Fu, Jian Shi, Mei Chung
Periodontal disease, which includes gingivitis and periodontitis, is highly prevalent in adults and disease severity increases with age. The relationship between periodontal disease and oral cancer has been examined for several decades, but there is increasing interest in the link between periodontal disease and overall cancer risk, with systemic inflammation serving as the main focus for biological plausibility. Numerous case-control studies have addressed the role of oral health in head and neck cancer, and several cohort studies have examined associations with other types of cancers over the past decade...
April 25, 2017: Epidemiologic Reviews
https://www.readbyqxmd.com/read/28448590/significant-changes-in-circulating-microrna-by-dietary-supplementation-of-selenium-and-coenzyme-q10-in-healthy-elderly-males-a-subgroup-analysis-of-a-prospective-randomized-double-blind-placebo-controlled-trial-among-elderly-swedish-citizens
#4
Urban Alehagen, Peter Johansson, Jan Aaseth, Jan Alexander, Dick Wågsäter
BACKGROUND: Selenium and coenzyme Q10 is essential for important cellular functions. A low selenium intake is reported from many European countries, and the endogenous coenzyme Q10 production is decreasing in the body with increasing age. Supplementation with selenium and coenzyme Q10 in elderly have shown reduced cardiovascular mortality and reduced levels of markers of inflammation. However, microRNA analyses could give important information on the mechanisms behind the clinical effects of supplementation...
2017: PloS One
https://www.readbyqxmd.com/read/28447720/p75-neurotrophin-receptor-a-potential-surface-marker-of-tongue-squamous-cell-carcinoma-stem-cells
#5
Dongdong Tong, Jing Sun, Ping Huang, Minqi Li, Fenghe Zhang
The present study detected p75 neurotrophin receptor (p75NTR) expression in tongue squamous cell carcinoma (TSCC) cell lines, in order to define the biological properties of p75NTR+ cells and to confirm the use of p75NTR+ as a surface marker for TSCC stem cells. p75NTR+ cells were separated from Tca‑8113 and CAL‑27 TSCC cells by fluorescence‑activated cell sorting. Colony formation, MTT and scratch assays, and a tumorigenicity analysis were performed to measure self-renewal and proliferation, multidirectional differentiation, and tumorigenicity of p75NTR+ cells...
March 7, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28446964/strategies-for-the-acquisition-of-transcriptional-and-epigenetic-information-in-single-cells
#6
REVIEW
Guang Li, Elda Dzilic, Nick Flores, Alice Shieh, Sean M Wu
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446714/profiling-of-metastatic-small-intestine-neuroendocrine-tumors-reveals-characteristic-mirnas-detectable-in-plasma
#7
Michaela Bowden, Chensheng W Zhou, Sui Zhang, Lauren Brais, Ashley Rossi, Laurent Naudin, Arunthi Thiagalingam, Ewa Sicinska, Matthew H Kulke
BACKGROUND: Current diagnostic and prognostic blood-based biomarkers for neuroendocrine tumors are limited. MiRNAs have tumor-specific expression patterns, are relatively stable, and can be measured in patient blood specimens. We performed a multi-stage study to identify and validate characteristic circulating miRNAs in patients with metastatic small intestine neuroendocrine tumors, and to assess associations between miRNA levels and survival. METHODS: Using a 742-miRNA panel, we identified candidate miRNAs similarly expressed in 19 small intestine neuroendocrine tumors and matched plasma samples...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445826/exposure-to-fine-particulate-matter-causes-oxidative-and-methylated-dna-damage-in-young-adults-a-longitudinal-study
#8
Ching-Huang Lai, Han-Bin Huang, Yue-Cune Chang, Ting-Yao Su, Ying-Chuan Wang, Gia-Chi Wang, Jia-En Chen, Chin-Sheng Tang, Trong-Neng Wu, Saou-Hsing Liou
An increased understanding is needed of the physiological effects and plausible biological mechanisms that link PM2.5 (particulate matter with an aerodynamic diameter below 2.5μm) exposure to mortality and morbidities such as atherosclerosis and respiratory disease. PM2.5 causes carcinogenic health effects. Biomonitoring in humans has suggested that 8-oxo-7, 8-dihydro-2-deoxyguanosine (8-oxodG) and N7-methylguanine (N7-MeG) are correlated with oxidative and methylated DNA damage. Thus, it is meaningful to explore the mechanisms of mutagenesis and carcinogenesis associated with oxidative and methylated DNA damage by simultaneously measuring these two markers...
April 23, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28445484/transcriptome-analysis-of-creeping-bentgrass-exposed-to-drought-stress-and-polyamine-treatment
#9
Yingmei Ma, Vijaya Shukla, Emily B Merewitz
Creeping bentgrass is an important cool-season turfgrass species sensitive to drought. Treatment with polyamines (PAs) has been shown to improve drought tolerance; however, the mechanism is not yet fully understood. Therefore, this study aimed to evaluate transcriptome changes of creeping bentgrass in response to drought and exogenous spermidine (Spd) application using RNA sequencing (RNA-Seq). The high-quality sequences were assembled and 18,682 out of 49,190 (38%) were detected as coding sequences. A total of 22% and 19% of genes were found to be either up- or down-regulated due to drought while 20% and 34% genes were either up- or down- regulated in response to Spd application under drought conditions, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28445399/advances-in-psychiatric-diagnosis-past-present-and-future
#10
EDITORIAL
Carol S North, Alina M Surís
This editorial examines controversies identified by the articles in this special issue, which explore psychopathology in the broad history of the classification of selected psychiatric disorders and syndromes over time through current American criteria. Psychiatric diagnosis has a long history of scientific investigation and application, with periods of rapid change, instability, and heated controversy associated with it. The articles in this issue examine the history of psychiatric nomenclature and explore current and future directions in psychiatric diagnosis through the various versions of accepted diagnostic criteria and accompanying research literature addressing the criteria...
April 26, 2017: Behavioral Sciences
https://www.readbyqxmd.com/read/28444666/markers-of-bone-and-cartilage-turnover
#11
Henning W Woitge, Markus J Seibel
Over the past few decades, scientists have been trying to identify tissue-specific markers that would help to better understand the pathogenesis of bone and cartilage diseases and could be used clinically for the screening, diagnosis and follow-up of bone or joint diseases. Historically, only a few components known to be involved in bone, mineral or cartilage turnover were available for this purpose (e. g., urine hydroxyproline, serum and urine calcium and phosphate levels). However, since most if not all of these substances have wider biological functions beyond bone, mineral and cartilage metabolism, their clinical value as tissue-specific markers was limited...
April 25, 2017: Experimental and Clinical Endocrinology & Diabetes
https://www.readbyqxmd.com/read/28443205/a-pilot-study-of-radiologic-measures-of-abdominal-adiposity-weighty-contributors-to-early-pancreatic-carcinogenesis-worth-evaluating
#12
Jennifer B Permuth, Jung W Choi, Dung-Tsa Chen, Kun Jiang, Gina DeNicola, Jian-Nong Li, Domenico Coppola, Barbara A Centeno, Anthony Magliocco, Yoganand Balagurunathan, Nipun Merchant, Jose G Trevino, Daniel Jeong
OBJECTIVE: Intra-abdominal fat is a risk factor for pancreatic cancer (PC), but little is known about its contribution to PC precursors known as intraductal papillary mucinous neoplasms (IPMNs). Our goal was to evaluate quantitative radiologic measures of abdominal/visceral obesity as possible diagnostic markers of IPMN severity/pathology. METHODS: In a cohort of 34 surgically-resected, pathologically-confirmed IPMNs (17 benign; 17 malignant) with preoperative abdominal computed tomography (CT) images, we calculated body mass index (BMI) and four radiologic measures of obesity: total abdominal fat (TAF) area, visceral fat area (VFA), subcutaneous fat area (SFA), and visceral to subcutaneous fat ratio (V/S)...
February 2017: Cancer Biology & Medicine
https://www.readbyqxmd.com/read/28443113/barcode-system-for-genetic-identification-of-soybean-glycine-max-l-merrill-cultivars-using-indel-markers-specific-to-dense-variation-blocks
#13
Hwang-Bae Sohn, Su-Jeong Kim, Tae-Young Hwang, Hyang-Mi Park, Yu-Young Lee, Kesavan Markkandan, Dongwoo Lee, Sunghoon Lee, Su-Young Hong, Yun-Ho Song, Bon-Cheol Koo, Yul-Ho Kim
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442506/genome-wide-association-studies-of-chemotherapeutic-toxicities-genomics-of-inequality
#14
Brandon Mapes, Omar El Charif, Shereen Al-Sawwaf, M Eileen Dolan
With an estimated global population of cancer survivors exceeding 32 million and growing, there is a heightened awareness of the long-term toxicities resulting from cancer treatments and their impact on quality of life. Unexplained heterogeneity in the persistence and development of toxicities, as well as an incomplete understanding of their mechanisms have generated a growing need for the identification of predictive pharmacogenomic markers. Early studies addressing this need used a candidate gene approach; however, over the last decade, unbiased and comprehensive genome-wide association studies (GWAS) have provided markers of phenotypic risk and potential targets to explore the mechanistic and regulatory pathways of biological functions associated with chemotherapeutic toxicity...
April 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28442449/comparative-proteomics-of-hydatid-fluids-from-two-echinococcus-multilocularis-isolates
#15
Karina M Monteiro, Karina R Lorenzatto, Jeferson C de Lima, Guilherme B Dos Santos, Sabine Förster, Gabriela P Paludo, Paulo C Carvalho, Klaus Brehm, Henrique B Ferreira
The hydatid fluid (HF) that fills Echinococcus multilocularis metacestode vesicles is a complex mixture of proteins from both parasite and host origin. Here, a LC-MS/MS approach was used to compare the HF composition of E. multilocularis H95 and G8065 isolates (EmH95 and EmG8065, respectively), which present differences in terms of growth and fertility. Overall, 446 unique proteins were identified, 392 of which (88%) were from parasite origin and 54 from culture medium. At least 256 of parasite proteins were sample exclusive, and 61 of the 136 shared proteins presented differential abundance between E...
April 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28442414/inhibition-of-allogeneic-cytotoxic-t-cell-cd8-proliferation-via-polymer-induced-treg-cd4-cells
#16
Ning Kang, Wendy M Toyofuku, Xining Yang, Mark D Scott
T cell-mediated immune rejection remains a barrier to successful transplantation. Polymer-based bioengineering of cells may provide an effective means of preventing allorecognition and the proliferation of cytotoxic (CD8(+)) T lymphocytes (CTL). Using MHC-disparate murine splenocytes modified with succinimidyl valerate activated methoxypoly(ethylene glycol) [SVA-mPEG] polymers, the effects of leukocyte immunocamouflage on CD8(+) and CD4(+) alloproliferation and T regulatory (Treg) cell induction were assessed in a mixed lymphocyte reaction (MLR) model...
April 22, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28442329/association-of-telomere-length-with-myocardial-infarction-a-prospective-cohort-from-the-population-based-hunt-2-study
#17
REVIEW
Ida Beate Øyen Østhus, Stian Lydersen, Håvard Dalen, Javaid Nauman, Ulrik Wisløff
As possible markers of biological age, telomere length (TL) has been associated with age-related diseases such as myocardial infarction (MI) with conflicting findings. We sought to assess the relationship between TL and risk of future MI in 915 healthy participants (51.7% women) 65 years or older from a population-based prospective cohort (the HUNT 2 study, Norway). Mean TL was measured by quantitative PCR expressed as relative T (telomere repeat copy number) to S (single copy gene number) ratio, and log-transformed...
April 22, 2017: Progress in Cardiovascular Diseases
https://www.readbyqxmd.com/read/28442243/abnormal-neural-precursor-cell-regulation-in-the-early-postnatal-fragile-x-mouse-hippocampus
#18
Mary Sourial, Laurie C Doering
The regulation of neural precursor cells (NPCs) is indispensable for a properly functioning brain. Abnormalities in NPC proliferation, differentiation, survival, or integration have been linked to various neurological diseases including Fragile X syndrome. Yet, no studies have examined NPCs from the early postnatal Fragile X mouse hippocampus despite the importance of this developmental time point, which marks the highest expression level of FMRP, the protein missing in Fragile X, in the rodent hippocampus and is when hippocampal NPCs have migrated to the dentate gyrus (DG) to give rise to lifelong neurogenesis...
April 22, 2017: Brain Research
https://www.readbyqxmd.com/read/28442213/pathogenic-cd4-t-cells-in-patients-with-asthma
#19
REVIEW
Lyndsey M Muehling, Monica G Lawrence, Judith A Woodfolk
Asthma encompasses a variety of clinical phenotypes that involve distinct T cell-driven inflammatory processes. Improved understanding of human T-cell biology and the influence of innate cytokines on T-cell responses at the epithelial barrier has led to new asthma paradigms. This review captures recent knowledge on pathogenic CD4(+) T cells in asthmatic patients by drawing on observations in mouse models and human disease. In patients with allergic asthma, TH2 cells promote IgE-mediated sensitization, airway hyperreactivity, and eosinophilia...
April 22, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28440611/the-meningioma-1-mn1-gene-is-an-independent-poor-prognostic-factor-in-adult-egyptian-acute-myeloid-leukemia-patients
#20
Roxan E Shafik, Naglaa M Hassan, Yomna M El Meligui, Hanan E Shafik
Aim: To determine the prognostic importance of meningioma 1 (MN1) gene expression levels in the context of other predictive markers for acute myeloid leukemia (AML) cases. Methods: MN1 expression was measured in 85 newly diagnosed adults younger than 60 years by real-time reverse-transcriptase polymerase chain reaction. Results: At diagnosis 67.4% of cases had elevated MN1 expression, this being associated with a worse prognosis, higher incidence of lymphadenopathy and CD34 transcript expression (p=0.02 and <0...
March 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
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